Lets assume we pass an $element that is a structured array, with parent and chil
d items. Both items have a theme function, generate output.

When we pass this arbitrary array to the render function, the parent element hit a content generation, and due to the content check after this rendering the child elements will depend upon having $content from the theme() or not.           
This might be avoided if we set the #children in the root item, however this is
not happening in the normal FAPI case, which makes me presume the normal operati
on of drupal_render is that parent element can not produce content.